User: Rory Stark

gravatar for Rory Stark
Rory Stark2.1k
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Location:
CRUK, Cambridge, UK
Last seen:
13 hours ago
Joined:
4 years, 8 months ago
Email:
r*********@cruk.cam.ac.uk

I am Principal Bioinformatics Analyst at the University of Cambridge, leading the Analysis Team in the Bioinformatics Core at Cancer Research UK's Cambridge Institute.

Posts by Rory Stark

<prev • 376 results • page 1 of 38 • next >
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Answer: A: DiffBind - Losing replicate information?
... Hi Sophie- Basically, if you don't have actual replicates you can't create them -- the multiple-peak-caller trick is only useful to capture some consensus peaks you might have otherwise missed, but once a consensus peakset is determined, we can only count overlapping reads once for each bam file. Y ...
written 13 hours ago by Rory Stark2.1k
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Answer: A: Multi-factor blocking in DiffBind
... You can specify multiple factors for blocking: > h3k27ac <- dba.contrast(h3k27ac, categories=DBA_CONDITION,   block=c(DBA_TISSUE,DBA_TREATMENT)) While this may be useful to get a quick look, it probably doesn't do what you really want however. It will create a facto ...
written 6 days ago by Rory Stark2.1k
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Answer: A: Pseudo-coloring DiffBind volcano plot
... I'm not sure what you mean in your first point, but the options for dba.plotVolcano() are fairly limited. You can call dba.report() to get all the data used in the plot to make your own more detailed plots. The axes labels in show exactly what is being plotted. Cheers- Rory ...
written 6 days ago by Rory Stark2.1k
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Answer: A: DiffBind DESeq2 MA plot skewed
... As Michael Love says, the diagonals represent sites that are at or near zero on one condition but have higher binding in the other. What is unusual is that the most dense part of the plot lies on one of these diagonals (sites with binding in group1 but no binding in group2). The usual dense area in ...
written 11 days ago by Rory Stark2.1k
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Answer: A: DiffBind error: diffbind DESeq2 analysis has not been run for this contrast
... It looks like the analysis did not get run for some reason. This can be seen by the fact that when you print out the DBA object after calling dba.analyze(), there are no columns for the number of differentially bound sites for DESeq2. Normally I would expect to see some error messages, but in some ...
written 13 days ago by Rory Stark2.1k
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Comment: C: Problem reading Bed file using dba.count in DiffBind
... The next step is to check the bed files to make sure they are well-formed. You are using 12 files, and there is some issue with 9 of them. I expect the warnings to state the name of the file which makes it easy to see which file shave a problem, but in this case we are seeing completely blank warnin ...
written 19 days ago by Rory Stark2.1k
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Comment: C: Principal component analysis produced by DiffBind, but PC1 with smaller variatio
... By default (bLog=TRUE), the read scores are first converted using log(). Then prcomp() is called with the log2 read score matrix. Only the data matrix is passed, no other parameters are set. Setting bLog=FALSE will pass in the read scores without calling log2() first. There is currently no way to c ...
written 21 days ago by Rory Stark2.1k
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Comment: C: Error message by dba.plotBox() function
... OK, I see what's going on. All of the differentially bound sites are + (fold change > 0; "gained"), and there are zero - ("loss") sites. DiffBind  generates the plot just fine, but is failing to detect this condition properly and generates an error when computing the p-values of the differences. ...
written 25 days ago by Rory Stark2.1k
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Answer: A: DiffBind broad and narrow peak identification
... In the example you show, while the fold-change difference is similar, there is quite a bit more variance in the second sample group, so it may not be surprising that it gets a higher p-value that gets more drastically adjusted by the FDR correction. You mention trying the summits option in dba.coun ...
written 25 days ago by Rory Stark2.1k
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Answer: A: MA plot DiffBind in ggplot2
... This is an artifact of reporting log values of normalized data. After normalization, some of the values may be less than one and hence will have negative log2 scores. So you are correct that if the normalized read counts for a peak in the replicates of one condition are very small (negative log valu ...
written 25 days ago by Rory Stark2.1k

Latest awards to Rory Stark

Scholar 4 months ago, created an answer that has been accepted. For A: DiffBind "no lines available in input" error
Guru 5 months ago, received more than 100 upvotes.
Popular Question 5 months ago, created a question with more than 1,000 views. For a diffBind problem
Scholar 5 months ago, created an answer that has been accepted. For A: DiffBind "no lines available in input" error
Popular Question 5 months ago, created a question with more than 1,000 views. For a diffBind problem
Scholar 8 months ago, created an answer that has been accepted. For A: DiffBind "no lines available in input" error
Scholar 8 months ago, created an answer that has been accepted. For A: DiffBind "no lines available in input" error
Autobiographer 13 months ago, has more than 80 characters in the information field of the user's profile.
Scholar 18 months ago, created an answer that has been accepted. For A: DiffBind "no lines available in input" error
Scholar 18 months ago, created an answer that has been accepted. For A: What does dba.PCA in DiffBind exactly do?
Scholar 18 months ago, created an answer that has been accepted. For A: DiffBind matrix of values
Scholar 18 months ago, created an answer that has been accepted. For A: ChIPQC and/or Diffbind - retrieving normalized read counts for peaks from single
Teacher 19 months ago, created an answer with at least 3 up-votes. For A: Work with GRanges objects in DiffBind
Scholar 20 months ago, created an answer that has been accepted. For A: What does dba.PCA in DiffBind exactly do?
Scholar 22 months ago, created an answer that has been accepted. For A: What does dba.PCA in DiffBind exactly do?
Scholar 23 months ago, created an answer that has been accepted. For A: What does dba.PCA in DiffBind exactly do?
Scholar 2.0 years ago, created an answer that has been accepted. For A: Work with GRanges objects in DiffBind
Teacher 2.0 years ago, created an answer with at least 3 up-votes. For A: diffBind correlation plot
Teacher 2.0 years ago, created an answer with at least 3 up-votes. For A: Work with GRanges objects in DiffBind
Scholar 2.0 years ago, created an answer that has been accepted. For A: diffBind correlation plot
Scholar 2.0 years ago, created an answer that has been accepted. For A: Clarification about the functionality of dba.count and dba.analyze
Scholar 2.0 years ago, created an answer that has been accepted. For A: subset of samples from dba object in DiffBind
Scholar 2.2 years ago, created an answer that has been accepted. For A: problem with characters in chromosome names in DiffBind dba
Teacher 2.2 years ago, created an answer with at least 3 up-votes. For A: diffBind correlation plot
Scholar 2.4 years ago, created an answer that has been accepted. For A: diffBind correlation plot

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